Gastrointestinal mucosal toxicity is extremely common following cytotoxic therapies. The alimentary mucosa is particularly susceptible to injury and dysfunction, leading to many debilitating complications. Despite much research, there is currently no single noninvasive biomarker to detect gut injury. Several biomarkers have been investigated in the context of gastrointestinal diseases, which may prove useful in the oncology arena. Identification of a biomarker that is easy to obtain and measure and that accurately identifies mucosal damage would allow for improved patient diagnosis of toxicities and for personalized treatment regimens. In this review, we highlight the effectiveness of urine and breath tests as potential clinically effective biomarkers, with significant focus placed on the emerging role of the carbon-13 sucrose breath test (13C SBT). The 13C SBT provides a simple, noninvasive, and integrated measure of gut function. The 13C SBT also has the potential to monitor gut function in the setting of cytotoxic therapy-induced mucositis, or in the assessment of the efficacy of antimucositis agents.